6V9P | pdb_00006v9p

Crystal structure of the transposition protein TniQ

PDB DOI: https://doi.org/10.2210/pdb6V9P/pdb

Classification: IMMUNE SYSTEM
Organism(s): Vibrio cholerae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-12-14 Released: 2020-01-29
Deposition Author(s): Jia, N., Patel, D.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.230 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structure-function insights into the initial step of DNA integration by a CRISPR-Cas-Transposon complex.

Jia, N., Xie, W., de la Cruz, M.J., Eng, E.T., Patel, D.J.

(2020) Cell Res 30: 182-184

PubMed: 31925391 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41422-019-0272-2
Primary Citation of Related Structures:
6V9P, 6V9Q, 6VBW

Organizational Affiliation

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. jian@mskcc.org.

Macromolecule Content

Total Structure Weight: 45.91 kDa
Atom Count: 3,113
Modeled Residue Count: 374
Deposited Residue Count: 395
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TniQ family protein	A	395	Vibrio cholerae	Mutation(s): 0 Gene Names: FXE93_08745
UniProt
Find proteins for A0A6I8WFW9 (Vibrio cholerae) Explore A0A6I8WFW9 Go to UniProtKB: A0A6I8WFW9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A6I8WFW9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL (Subject of Investigation/LOI) Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free: 0.262 (Depositor), 0.260 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.822	α = 90
b = 69.822	β = 90
c = 179.491	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2020-01-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2020-01-29
Type: Initial release
Version 1.1: 2020-02-19
Changes: Database references
Version 1.2: 2024-03-06
Changes: Data collection, Database references

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.